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College of American Pathologists. Molecular pathology checklist. Available at: http://www.cap.org/apps/docs/laboratory_accreditation/checklists/new/molecular_pathology_checklist.pdf. Accessed on June, 28, 2013.
- Nucleic Acid Sequencing Methods in Diagnostic Laboratory Medicine; Approved Guideline. CLSI document MM9-A.Clinical and Laboratory Standards Institute, Wayne, Pennsylvania2004
New York State Department of Health. “Next Generation” Sequencing (NGS) Guidelines for Somatic Genetic Variant Detection. Available at: http://www.wadsworth.org/labcert/TestApproval/forms/NextGenSeq_ONCO_Guidelines.pdf. Accessed on June, 28, 2013.
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- Molecular Subcommittee of the ALQAC. ACMG recommendations for standards for interpretation and reporting of sequence variations: revisions 2007.Genet Med. 2008; 10: 294-300
- Targeted, high-depth, next generation sequencing of cancer genes in formalin-fixed, paraffin-embedded and fine-needle aspiration tumor specimens.J Mol Diagn. 2013; 15: 234-247
- ColoSeq provides comprehensive lynch and polyposis syndrome mutational analysis using massively parallel sequencing.J Mol Diagn. 2012; 14: 357-366
- Target-enrichment strategies for next generation sequencing.Nat Methods. 2010; 7: 111-118
- Whole exome capture in solution with 3 Gbp of data.Genome Biol. 2010; 11: R62
- Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing.Nat Biotechnol. 2009; 27: 182-189
Ernani FP, LeProust EM. Agilent’s SureSelect target enrichment system: bringing cost and process efficiency to next generation sequencing. Available at: http://www.chem.agilent.com/Library/brochures/5990-3532en_lo%20CMS.pdf. Accessed on May, 21, 2013.
- Comparison of solution-based exome capture methods for next generation sequencing.Genome Biol. 2011; 12: R94
Life Technologies. Ion TargetSeq custom enrichment kits: user guide. Available at: http://tools.lifetechnologies.com/content/sfs/manuals/IonTargetSeq_Custom_UG.pdf. Accessed on November, 6, 2013.
- Integration of next generation sequencing into clinical practice: are we there yet?.Semin Oncol. 2012; 39: 26-36
- Nanofluidic digital PCR for KRAS mutation detection and quantification in gastrointestinal cancer.Clin Chem. 2012; 58: 1332-1341
- Noninvasive identification and monitoring of cancer mutations by targeted deep sequencing of plasma DNA.Sci Transl Med. 2012; 4: 136ra68
- Targeted enrichment of genomic DNA regions for next generation sequencing.Brief Funct Genomics. 2011; 10: 374-386
Fluidigm Corporation. Sequencing: from sample to sequence ready. Available at: http://www.fluidigm.com/home/fluidigm/images/products/access_array_final_post.pdf. Accessed on November, 6, 2013.
RainDance Technologies. RainDance ThunderStorm System [product brief]. Available at: http://www.raindancetech.com/rdt/wp-content/uploads/downloads/product-brief_thunderstorm.pdf. Accessed on November, 6, 2013.
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Agilent Technologies. HaloPlex Target Enrichment System for Illumina sequencing [protocol]. Available at: http://www.chem.agilent.com/Library/usermanuals/Public/G9900-90000.pdf. Accessed on November, 6, 2013.
Illumina Inc. Sequencing: TruSeq amplicon—cancer panel [data sheet]. Available at: http://res.illumina.com/documents/products/datasheets/datasheet_truseq_amplicon_cancer_panel.pdf. Accessed on November, 6, 2013.
Life Technologies. Ion AmpliSeq comprehensive cancer panel. Available at: http://tools.lifetechnologies.com/content/sfs/brochures/Ion_CompCancerPanel_Flyer.pdf. Accessed on November, 6, 2013.
College of American Pathologists. Laboratory general checklist. Available at: http://www.cap.org/apps/docs/laboratory_accreditation/checklists/new/laboratory_general_checklist.pdf. Accessed on November, 6, 2013.
- Rate of occult specimen provenance complications in routine clinical practice.Am J Clin Pathol. 2013; 139: 93-100
- DNA isolation from mammalian samples.Curr Protoc Mol Biol. 2013; 102 (2.14.1-2.14.13)
- Microvolume quantitation of nucleic acids.Curr Protoc Mol Biol. 2011; 93 (A.3J.1-A.3J.16)
- Quantitation of DNA and RNA with absorption and fluorescence spectroscopy.Curr Protoc Protein Sci. 2008; 52 (A.4K.1-A.4K.21)
- Overview of DNA sequencing strategies.Curr Protoc Mol Biol. 2011; 96 (7.1.1-7.1.23)
Agilent Technologies. SureSelect target enrichment system for Illumina paired-end sequencing library [protocol]. Available at: http://www.genomics.agilent.com/files/Manual/G3360-90020_SureSelect_Indexing_1.0.pdf. Accessed on May, 21, 2013.
- Clinical genomicist workstation.AMIA Summits Transl Sci Proc. 2013; 2013: 156-157
- Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences.Genome Biol. 2010; 11: R86
- The Genome Analysis Toolkit: a MapReduce framework for analyzing next generation DNA sequencing data.Genome Res. 2010; 20: 1297-1303
- Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads.Bioinformatics. 2009; 25: 2865-2871
- SOAPindel: efficient identification of indels from short paired reads.Genome Res. 2013; 23: 195-200
- Low concordance of multiple variant-calling pipelines: practical implications for exome and genome sequencing.Genome Med. 2013; 5: 28
- A survey of copy-number variation detection tools based on high-throughput sequencing data.Curr Protoc Hum Genet. 2012; 75 (7.19.1-7.19.15)
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- Increased efficiency of mRNA 3' end formation: a new genetic mechanism contributing to hereditary thrombophilia.Nat Genet. 2001; 28: 389-392
- APC germline mutations in individuals being evaluated for familial adenomatous polyposis: a review of the Mayo Clinic experience with 1591 consecutive tests.J Mol Diagn. 2013; 15: 31-43
Wellcome Trust Sanger Institute. COSMIC: Catalogue of Somatic Mutations in Cancer. Available at: http://cancer.sanger.ac.uk/cancergenome/projects/cosmic/. Accessed on December 24, 2013.
National Center for Biotechnology Information. dbSNP. Available at: http://www.ncbi.nlm.nih.gov/projects/SNP/. Accessed on December 24, 2013.
National Heart, Lung, and Blood Institute. NHLBI GO Exome Sequencing Project (ESP): Exome Variant Server. Available at: (http://evs.gs.washington.edu/EVS/). Accessed on December 24, 2013.
- Epidermal growth factor receptor R521K polymorphism shows favorable outcomes in KRAS wild-type colorectal cancer patients treated with cetuximab-based chemotherapy.Cancer Sci. 2012; 103: 791-796
- The c-kit (CD117) sequence variation M541L, but not N564K, is frequent in the general population, and is not associated with CML in Caucasians.Leukemia. 2006; 20 (discussion 356–357): 354-355
- p53 polymorphisms: cancer implications.Nat Rev Cancer. 2009; 9: 95-107
- Point-counterpoint. Patient autonomy and incidental findings in clinical genomics.Science. 2013; 340: 1049-1050
- Lung adenocarcinoma: guiding EGFR-targeted therapy and beyond.Mod Pathol. 2008; 21: S16-S22
- Integrating common and rare genetic variation in diverse human populations.Nature. 2010; 467: 52-58
- A map of human genome variation from population-scale sequencing.Nature. 2010; 467: 1061-1073
- Human genome sequencing using unchained base reads on self-assembling DNA nanoarrays.Science. 2010; 327: 78-8153
- Validation of a next-generation sequencing assay for clinical molecular oncology.J Mol Diagn. 2014; 16 (Epub 2013 Nov 6): 89-105https://doi.org/10.1016/j.jmoldx.2013.10.002